mass_spectrum.molecular_search_settings.isRadical = False
mass_spectrum.molecular_search_settings.isAdduct = True
SearchMolecularFormulas(mass_spectrum,
first_hit=False).run_worker_mass_spectrum()
mass_spectrum.percentile_assigned()
mass_spectrum_by_classes = HeteroatomsClassification(
mass_spectrum, choose_molecular_formula=False)
mass_spectrum_by_classes.plot_ms_assigned_unassigned()
plt.show()
all_classes = 0
for classe in mass_spectrum_by_classes.get_classes(threshold_perc=0,
isotopologue=True):
mass_spectrum_by_classes.plot_dbe_vs_carbon_number(classe)
#plt.show()
mass_spectrum_by_classes.plot_ms_class(classe)
plt.show()
mass_spectrum_by_classes.plot_mz_error_class(classe)
mz_calc_l = mass_spectrum_by_classes.mz_calc(classe)
mf_l = mass_spectrum_by_classes.molecular_formula(classe)
print(
"# Name; m/z value; charge; ion formula; collision cross section [A^2]"
def create_plots(mass_spectrum, workflow_params, dirloc):
ms_by_classes = HeteroatomsClassification(mass_spectrum,
choose_molecular_formula=False)
if workflow_params.plot_ms_assigned_unassigned:
print("Plotting assigned vs. unassigned mass spectrum")
ax_ms = ms_by_classes.plot_ms_assigned_unassigned()
plt.savefig(dirloc / "assigned_unassigned.png", bbox_inches='tight')
plt.clf()
if workflow_params.plot_mz_error:
print("Plotting mz_error")
ax_ms = ms_by_classes.plot_mz_error()
plt.savefig(dirloc / "mz_error.png", bbox_inches='tight')
plt.clf()
if workflow_params.plot_van_krevelen:
van_krevelen_dirloc = dirloc / "van_krevelen"
van_krevelen_dirloc.mkdir(exist_ok=True, parents=True)
if workflow_params.plot_c_dbe:
c_dbe_dirloc = dirloc / "dbe_vs_c"
c_dbe_dirloc.mkdir(exist_ok=True, parents=True)
if workflow_params.plot_ms_classes:
ms_class_dirloc = dirloc / "ms_class"
ms_class_dirloc.mkdir(exist_ok=True, parents=True)
if workflow_params.plot_mz_error_classes:
mz_error_class_dirloc = dirloc / "mz_error_class"
mz_error_class_dirloc.mkdir(exist_ok=True, parents=True)
pbar = tqdm(ms_by_classes.get_classes())
for classe in pbar:
pbar.set_description_str(
desc="Plotting results for class {}".format(classe), refresh=True)
if workflow_params.plot_van_krevelen:
ax_c = ms_by_classes.plot_van_krevelen(classe)
plt.savefig(van_krevelen_dirloc / "{}.png".format(classe),
bbox_inches='tight')
plt.clf()
if workflow_params.plot_mz_error_classes:
ax_c = ms_by_classes.plot_mz_error_class(classe)
plt.savefig(mz_error_class_dirloc / "{}.png".format(classe),
bbox_inches='tight')
plt.clf()
if workflow_params.plot_ms_classes:
ax_c = ms_by_classes.plot_ms_class(classe)
plt.savefig(ms_class_dirloc / "{}.png".format(classe),
bbox_inches='tight')
plt.clf()
if workflow_params.plot_c_dbe:
ax_c = ms_by_classes.plot_dbe_vs_carbon_number(classe)
plt.savefig(c_dbe_dirloc / "{}.png".format(classe),
bbox_inches='tight')
plt.clf()